Hydrogen atoms affect the dislocation core causing the plastic deformation to localize and thus to decrease the material capacity for plastic deformation. Better understanding of the role of hydrogen will lead to reliable computational models that incorporate hydrogen effects and diffusion through dislocation-densities evolution laws. Here we present large scale molecular dynamics simulations of the dislocation-density evolution and surface morphology in pillar like iron nano-crystals. Several nanopillar sizes are modeled having sizes of 20x20x40, 40x40x60 and 100x100x100 nm^3. An initial dislocation network is introduced using the anisotropic displacement field. Hydrogen atoms with different concentrations are randomly distributed in the crystals. The interrelated effects of size, initial dislocation-density, loading direction, and hydrogen concentration are thoroughly investigated. The effect of hydrogen concentration on yielding, retention of dislocations, and the morphology of surface slip is also discussed in details.